Mercurial > repos > metexplore > met4j
comparison build/tools/NetworkSummary/NetworkSummary.xml @ 6:7a6f2380fc1d draft
planemo upload for repository https://forgemia.inra.fr/metexplore/met4j-galaxy
| author | metexplore |
|---|---|
| date | Wed, 17 May 2023 13:26:37 +0000 |
| parents | |
| children | 1436e9cde9c9 |
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| 5:35c9abcd8934 | 6:7a6f2380fc1d |
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| 1 <?xml version="1.0" encoding="UTF-8"?> | |
| 2 <tool id="met4j_NetworkSummary" name="NetworkSummary" version="1.3.0"> | |
| 3 <description>Create a report summarizing several graph measures characterising the structure of the network.</description> | |
| 4 <xrefs> | |
| 5 <xref type="bio.tools">met4j</xref> | |
| 6 </xrefs> | |
| 7 <requirements> | |
| 8 <container type="singularity">oras://registry.forgemia.inra.fr/metexplore/met4j/met4j-singularity:1.3.0</container> | |
| 9 </requirements> | |
| 10 <command detect_errors="exit_code"><![CDATA[sh /usr/bin/met4j.sh networkAnalysis.NetworkSummary -i "$inputPath" | |
| 11 #if str($sideCompoundFile) != 'None': | |
| 12 -s "$sideCompoundFile" | |
| 13 #end if | |
| 14 $skipdist | |
| 15 $directed | |
| 16 -o "$outputPath" | |
| 17 ]]></command> | |
| 18 <inputs> | |
| 19 <param argument="-i" format="sbml" label="input SBML file" name="inputPath" optional="false" type="data" value=""/> | |
| 20 <param argument="-s" format="txt" label="an optional file containing list of side compounds to ignore (recommended)" name="sideCompoundFile" optional="true" type="data" value=""/> | |
| 21 <param argument="-sd" checked="false" falsevalue="" label="skip full distance matrix computation (quick summary)" name="skipdist" truevalue="-sd" type="boolean" value="false"/> | |
| 22 <param argument="-d" checked="false" falsevalue="" label="use reaction direction for distances" name="directed" truevalue="-d" type="boolean" value="false"/> | |
| 23 </inputs> | |
| 24 <outputs> | |
| 25 <data format="txt" name="outputPath"/> | |
| 26 </outputs> | |
| 27 <tests> | |
| 28 <test> | |
| 29 <param name="inputPath" value="toy_model.xml"/> | |
| 30 <output name="outputPath"> | |
| 31 <assert_contents> | |
| 32 <has_n_lines min="1"/> | |
| 33 </assert_contents> | |
| 34 </output> | |
| 35 </test> | |
| 36 </tests> | |
| 37 <help><![CDATA[Use a metabolic network in SBML file and an optional list of side compounds, and produce a report summarizing several graph measures characterising the structure of the network.This includes (non-exhaustive list): size and order, connectivity, density, degree distribution, shortest paths length, top centrality nodes...]]></help> | |
| 38 <citations/> | |
| 39 </tool> |